mzID

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 1.50.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: XML, plyr, doParallel, foreach, iterators, ProtGenerics
• System requirements: URL
• Install: BiocManager::install("mzID")

When to Use

• Parsing mzIdentML Files: Reading HUPO-PSI standard mzIdentML (.mzid) files containing peptide and protein identification results using the mzID() function.
• Data Flattening: Converting complex, nested structures of mzIdentML files into flat, easy-to-manipulate R data.frame objects using the flatten() function.
• Metadata Extraction: Extracting search database details, peptide-spectrum matches (PSMs), and search engine scores for downstream custom analysis.

When NOT to Use

• For parsing raw mass spectrometry spectra (mzML, mzXML) or quantitative data (mzQuantML), use mzR instead because mzID only parses identification files.
• For high-level quantitative proteomics data manipulation, use MSnbase instead because mzID is strictly a barebones parser for identification data.

Data Requirements

• Input: Valid mzIdentML (.mzid) files conforming to the HUPO-PSI schema.
• Structure: The parsed mzID object contains slots for parameters, psm, peptides, evidence, and database.

Key Parameters

• file: Path to the mzIdentML file to be parsed (passed as the first argument to mzID()).